Bringing large scale top-down metabolic modelling to eukaryotes with PhotoEukStein: a meta-model for unicellular phototrophs

Abstract

Defining biological functional traits for unicellular organisms relies on comprehending the set and combination of the biochemical reactions their genomes encode for. This network of biochemical reactions defines the metabolic strategy organisms and communities use. Understanding the functional traits of unicellular organisms involves studying the combination of biochemical reactions encoded in their genomes. These reactions determine the metabolic strategy that organisms and communities use to grow in a specific environment. While prokaryotes have been extensively studied for their metabolic networks, eukaryotes have lagged behind due to the complexity of their genomes and the need for a better understanding of their metabolism. We have created PhotoEukstein, a meta-metabolic model for unicellular phototrophic eukaryotes. This meta-model enables quick and automated derivation of Genome-Scale Metabolic models directly from genomes. We have used it to analyse 533 environmental genomes and marine eukaryotic unicellular plankton transcriptomes. These models can help predict functional traits that cannot be purely deducted from taxonomic information or the listing of metabolic reactions encoded by the genome. They provide the opportunity to build connections with Earth System Models to pinpoint environmental parameters to capture specific functional traits.